org.strbio.mol.lib
Class DayhoffMatrices

java.lang.Object
  org.strbio.mol.lib.DayhoffMatrices

public class DayhoffMatrices
extends java.lang.Object

Dayhoff matrices (various)

  Dayhoff, MO
  1978
  Atlas of Protein Sequence and Structure
  volume 5, #3
  p. 353 - 358.
  

All numbers translate to AA's according to: ARNDCQEGHILKMFPSTWYV

Version:

1.0

Author:

JMC

See Also:

Residue

Constructor Summary

DayhoffMatrices()

Method Summary

static DVector	DayhoffFreq() Dayhoff frequencies for each amino acid.
static DMatrix	DayhoffMdm78() Dayhoff mutation data matrix 78.
static DMatrix	DayhoffPam250() Dayhoff, MO 1978 Atlas of Protein Sequence and Structure volume 5, #3 p. 353 - 358.
static DMatrix	DayhoffRelatednessOdds() Dayhoff relatedness odds matrix.
static DMatrix	GribskovBurgess() g_b matrix used in: mclachlan, eisenberg - PNAS 84:4355 - 4358 Gribskov & Burgess 1986 Nucleic Acid Research vol 14 p 6745 - 6763 this is mdm78, adjusted to have mean of 0, and sd of 1.
static DMatrix	Mclachlan() mclachlan matrix described in: McLachlan Andrew D.
static DMatrix	Sander() Some Sander matrix, for which I don't have the reference.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

DayhoffMatrices

public DayhoffMatrices()

Method Detail

DayhoffPam250

public static final DMatrix DayhoffPam250()

      Dayhoff, MO
      1978
      Atlas of Protein Sequence and Structure
      volume 5, #3
      p. 353 - 358.
      

DayhoffFreq

public static final DVector DayhoffFreq()

Dayhoff frequencies for each amino acid.

DayhoffRelatednessOdds

public static final DMatrix DayhoffRelatednessOdds()

Dayhoff relatedness odds matrix.

DayhoffMdm78

public static final DMatrix DayhoffMdm78()

Dayhoff mutation data matrix 78.

GribskovBurgess

public static final DMatrix GribskovBurgess()

g_b matrix used in: mclachlan, eisenberg - PNAS 84:4355 - 4358

      Gribskov & Burgess
      1986
      Nucleic Acid Research
      vol 14
      p 6745 - 6763
      

this is mdm78, adjusted to have mean of 0, and sd of 1. identical residues all score 1.5

Mclachlan

public static final DMatrix Mclachlan()

mclachlan matrix described in:

      McLachlan Andrew D.
      Tests for comparing related amino acid sequences.
      J.Mol.Biol.
      61,409-424, minimal.
      

1971 value: -3.0 ; maximal value: 6.0

Sander

public static final DMatrix Sander()

Some Sander matrix, for which I don't have the reference.